How does --primary work with -M and --fractional options featureCounts?
1
0
Entering edit mode
2.3 years ago
Lucy ▴ 140

Hi,

I am trying to understand how the -M, --primary and --fractional work together in featureCounts. From my understanding, -M is ignored if you add the --primary flag. However, what setting should I use if I want to count primary alignments fractionally? Some reads have multiple primary alignments since I have set --outSAMprimaryFlag to AllBestScore in STAR, so all alignments with the best score will be output as primary alignments.

Best wishes,

Lucy

RNA-seq subread mapping featureCounts STAR • 583 views
ADD COMMENT
0
Entering edit mode
2.3 years ago

If you want full control over the alignments then I would recommend filtering the BAM file prior to counting.

In your case make a new BAM file that contains only the primary alignments.

ADD COMMENT
0
Entering edit mode

Yes I could do this and then use -M and --fractional within featureCounts. Is that what you are suggesting?

ADD REPLY

Login before adding your answer.

Traffic: 2463 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6